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https://www.readbyqxmd.com/read/28723513/the-natural-history-and-outcome-predictors-of-metastatic-castration-resistant-prostate-cancer
#1
REVIEW
Robert J van Soest, Jason A Efstathiou, Cora N Sternberg, Bertand Tombal
CONTEXT: Biomarkers for the treatment of metastatic castration-resistant prostate cancer (mCRPC) are urgently needed by clinicians to facilitate treatment decisions. OBJECTIVE: To review current prognostic and predictive biomarkers in mCRPC. EVIDENCE ACQUISITION: We performed a nonsystematic review of the literature from 2004 to August 2016 by searching in Medline. Cross-matching references were used to search for additional articles. We reviewed clinical research and review articles written in the English language...
December 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#2
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28720677/synthetic-circulating-cell-free-dna-as-quality-control-materials-for-somatic-mutation-detection-in-liquid-biopsy-for-cancer
#3
Rui Zhang, Rongxue Peng, Ziyang Li, Peng Gao, Shiyu Jia, Xin Yang, Jiansheng Ding, Yanxi Han, Jiehong Xie, Jinming Li
BACKGROUND: Detection of somatic genomic alterations in tumor-derived cell-free DNA (cfDNA) in the plasma is challenging owing to the low concentrations of cfDNA, variable detection methods, and complex workflows. Moreover, no proper quality control materials are available currently. METHODS: We developed a set of synthetic cfDNA quality control materials (SCQCMs) containing spike-in cfDNA on the basis of micrococcal nuclease digestion carrying somatic mutations as simulated cfDNA and matched genomic DNA as genetic background to emulate paired tumor-normal samples in real clinical tests...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28714327/elevated-levels-of-circulating-cell-free-dna-and-neutrophil-proteins-are-associated-with-neonatal-sepsis-and-necrotizing-enterocolitis-in-immature-mice-pigs-and-infants
#4
Duc Ninh Nguyen, Allan Stensballe, Jacqueline Cy Lai, Pingping Jiang, Anders Brunse, Yanqi Li, Jing Sun, Carina Mallard, Tom Skeath, Nicholas D Embleton, Janet E Berrington, Per T Sangild
Preterm infants are highly susceptible to late-onset sepsis (LOS) and necrotizing enterocolitis (NEC), but disease pathogenesis and specific diagnostic markers are lacking. Circulating cell-free DNA (cfDNA) and immune cell-derived proteins are involved in multiple immune diseases in adults but have not been investigated in preterm neonates. We explored the relation of circulating neutrophil-associated proteins and cfDNA to LOS and/or NEC. Using a clinically relevant preterm pig model of spontaneous LOS and NEC development, we investigated neutrophil-associated proteins and cfDNA in plasma, together with cytokines in gut tissues...
January 1, 2017: Innate Immunity
https://www.readbyqxmd.com/read/28710315/shallow-whole-genome-sequencing-on-circulating-cell-free-dna-allows-reliable-non-invasive-copy-number-profiling-in-neuroblastoma-patients
#5
Nadine Van Roy, Malaika Van der Linden, Björn Menten, Annelies Dheedene, Charlotte Vandeputte, Jo Van Dorpe, Geneviève Laureys, Marleen Renard, Tom Sante, Tim Lammens, Bram De Wilde, Frank Speleman, Katleen De Preter
<p>Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of NB patients could offer a valuable alternative to primary tumor DNA for CNA profiling.</p> <br /><br />Experimental Design: <p>In 37 NB patients cfDNA analysis using shallow whole genome sequencing (sWGS) was compared to arrayCGH analysis of primary tumor tissue...
July 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28707075/line-1-hypermethylation-in-serum-cell-free-dna-of-relapsing-remitting-multiple-sclerosis-patients
#6
Marina Dunaeva, Merel Derksen, Ger J M Pruijn
Concentrations of cell-free DNA (cfDNA) circulating in blood and its epigenetic variation, such as DNA methylation, may provide useful diagnostic or prognostic information. Long interspersed nuclear element-1 (LINE-1) constitutes approximately 20% of the human genome and its 5'UTR region is CpG rich. Due to its wide distribution, the methylation level of the 5'UTR of LINE-1 can serve as a surrogate marker of global genomic DNA methylation. The aim of the current study was to investigate whether the methylation status of LINE-1 elements in serum cell-free DNA differs between relapsing remitting multiple sclerosis (RRMS) patients and healthy control subjects (CTR)...
July 13, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28702698/principles-of-first-trimester-screening-in-the-age-of-non-invasive-prenatal-diagnosis-screening-for-chromosomal-abnormalities
#7
REVIEW
Karl Oliver Kagan, Jiri Sonek, Philipp Wagner, Markus Hoopmann
PURPOSE: First trimester risk assessment for chromosomal abnormalities plays a major role in the contemporary pregnancy care. It has evolved significantly since its introduction in the 1990s, when it essentially consisted of just the nuchal translucency measurement. Today, it involves the measurement of several biophysical and biochemical markers and it is often combined with a cell-free DNA (cfDNA) analysis as a secondary test. METHODS: A search of the Medline and Embase databases was done looking for articles about first trimester aneuploidy screening...
July 12, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28692984/a-study-of-cell-free-dna-fragmentation-pattern-and-its-application-in-dna-sample-type-classification
#8
Shifu Chen, Ming Liu, Xiaoni Zhang, Renwen Long, Yixing Wang, Yue Han, Shiwei Zhang, Mingyan Xu, Jia Gu
Plasma cell-free DNA (cfDNA) has certain fragmentation patterns, which can bring non-random base content curves of the sequencing data's beginning cycles. We studied the patterns and found that we could determine whether a sample is cfDNA or not by just looking into the first 10 cycles of its base content curves. We analysed 3189 FastQ files, including 1442 cfDNA, 1234 genomic DNA, 507 FFPE tumour DNA and 6 urinary cfDNA. By deep analysing these data, we find the patterns are stable enough to distinguish cfDNA from other kinds of DNA samples...
July 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28692178/cell-free-dna-minimally-invasive-marker-of-hematological-malignancies
#9
REVIEW
V Kubaczkova, D Vrabel, L Sedlarikova, L Besse, S Sevcikova
Although tumor cells are the most reliable source of tumor DNA, biopsy of the tumor is an invasive procedure that should be avoided in some cases. The main limitation of any biopsy is sampling of one tumor site, which may not represent all malignant clones due to the heterogeneity of the tumor. These clones respond to treatment differently and thus directly influence survival of the patient. Circulating cell-free DNA (cfDNA) is released from multiple tumor sites, reflects overall heterogeneity of the tumor and correlates with its progression...
July 10, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/28691390/an-improved-digital-polymerase-chain-reaction-protocol-to-capture-low-copy-kras-mutations-in-plasma-cell-free-dna-by-resolving-subsampling-issues
#10
REVIEW
Yusuke Ono, Ayumu Sugitani, Hidenori Karasaki, Munehiko Ogata, Reo Nozaki, Junpei Sasajima, Tomoki Yokochi, Shingo Asahara, Kazuya Koizumi, Kiyohiro Ando, Katsunori Hironaka, Tsutomu Daito, Yusuke Mizukami
Genetic alterations responsible for the initiation of cancer may serve as immediate biomarkers for early diagnosis. Plasma levels of cell-free DNA (cfDNA) in cancer patients are higher than those in healthy individuals, however, the major technical challenge for the widespread implementation of cfDNA genotyping as a diagnostic tool is the insufficient sensitivity and specificity of detecting early-stage tumors that shed low amounts of cfDNA. To establish a protocol for ultrasensitive droplet digital polymerase chain reaction (ddPCR) for quantification of low-frequency alleles within a limited cfDNA pool, two-step multiplex ddPCR targeting eight clinically relevant mutant KRAS variants was examined...
July 10, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28686671/assessment-of-circulating-copy-number-variant-detection-for-cancer-screening
#11
Bhuvan Molparia, Eshaan Nichani, Ali Torkamani
Current high-sensitivity cancer screening methods, largely utilizing correlative biomarkers, suffer from false positive rates that lead to unnecessary medical procedures and debatable public health benefit overall. Detection of circulating tumor DNA (ctDNA), a causal biomarker, has the potential to revolutionize cancer screening. Thus far, the majority of ctDNA studies have focused on detection of tumor-specific point mutations after cancer diagnosis for the purpose of post-treatment surveillance. However, ctDNA point mutation detection methods developed to date likely lack either the scope or analytical sensitivity necessary to be useful for cancer screening, due to the low (<1%) ctDNA fraction derived from early stage tumors...
2017: PloS One
https://www.readbyqxmd.com/read/28683468/correlation-between-circulating-mutant-dna-and-metabolic-tumour-burden-in-advanced-non-small-cell-lung-cancer-patients
#12
Anne Winther-Larsen, Christina Demuth, Joan Fledelius, Anne Tranberg Madsen, Karin Hjorthaug, Peter Meldgaard, Boe Sandahl Sorensen
BACKGROUND: Mutated circulating cell-free DNA (cfDNA) has been suggested as a surrogate marker of tumour burden and aggressiveness of disease. We examined the association between the level of plasma mutant cfDNA and metabolic tumour burden (MTB) measured by (18)F-fluoro-D-glucose positron emission tomography/computed tomography ((18)F-FDG PET/CT). Furthermore, the presence of mutant cfDNA was correlated with patient survival. METHODS: Forty-six advanced non-small cell lung cancer (NSCLC) patients were included...
July 6, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28679775/detection-of-activating-estrogen-receptor-gene-esr1-mutations-in-single-circulating-tumor-cells
#13
Carmela Paolillo, Zhaomei Mu, Giovanna Rossi, Matthew J Schiewer, Thomas Nguyen, Laura Austin, Ettore Capoluongo, Karen E Knudsen, Massimo Cristofanilli, Paolo Fortina
Early detection is essential for treatment plans before onset of metastatic disease. Our purpose was to demonstrate feasibility to detect and monitor estrogen receptor 1 (ESR1) gene mutations at the single circulating tumor cell (CTC) level in metastatic breast cancer (MBC). <br /><br />Experimental Design: We used a CTC molecular characterization approach to investigate heterogeneity of 14 hot spot mutations in ESR1 and their correlation with endocrine resistance. Combining the CellSearch(®) and DEPArray™ technologies allowed recovery of 71 single CTCs and 12 WBC from 3 ER-positive MBC patients...
July 5, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28679646/multiplexed-elimination-of-wild-type-dna-and-high-resolution-melting-prior-to-targeted-resequencing-of-liquid-biopsies
#14
Ioannis Ladas, Mariana Fitarelli-Kiehl, Chen Song, Viktor A Adalsteinsson, Heather A Parsons, Nancy U Lin, Nikhil Wagle, G Mike Makrigiorgos
BACKGROUND: The use of clinical samples and circulating cell-free DNA (cfDNA) collected from liquid biopsies for diagnostic and prognostic applications in cancer is burgeoning, and improved methods that reduce the influence of excess wild-type (WT) portion of the sample are desirable. Here we present enrichment of mutation-containing sequences using enzymatic degradation of WT DNA. Mutation enrichment is combined with high-resolution melting (HRM) performed in multiplexed closed-tube reactions as a rapid, cost-effective screening tool before targeted resequencing...
July 5, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28672797/integrity-and-quantity-of-total-cell-free-dna-in-the-diagnosis-of-thyroid-cancer-correlation-with-cytological-classification
#15
Francesca Salvianti, Corinna Giuliani, Luisa Petrone, Irene Mancini, Vania Vezzosi, Cinzia Pupilli, Pamela Pinzani
Cell-free DNA (cfDNA) quantity and quality in plasma has been investigated as a non-invasive biomarker in cancer. Previous studies have demonstrated increased cfDNA amount and length in different types of cancer with respect to healthy controls. The present study aims to test the hypothesis that the presence of longer DNA strands circulating in plasma can be considered a biomarker for tumor presence in thyroid cancer. We adopted a quantitative real-time PCR (qPCR) approach based on the quantification of two amplicons of different length (67 and 180 bp respectively) to evaluate the integrity index 180/67...
June 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28668269/valproic-acid-alters-the-content-and-function-of-the-cell-free-dna-released-by-hepatocellular-carcinoma-hepg2-cells-in-vitro
#16
Janine Aucamp, Hayley C Van Dyk, Abel J Bronkhorst, Piet J Pretorius
BACKGROUND: It has long been believed that cell-free DNA (cfDNA) actively released into circulation can serve as intercellular messengers, and their involvement in processes such as the bystander effect strongly support this. However, this intercellular messaging function of cfDNA may have clinical implications that have not yet been considered. METHODS: CfDNA was isolated from the growth medium of HepG2 cells treated with valproic acid (VPA). This cfDNA was then administered to untreated cells and cellular metabolic activity was measured...
June 28, 2017: Biochimie
https://www.readbyqxmd.com/read/28667367/platelets-circulating-tumor-cells-and-the-circulome
#17
REVIEW
Preeti Kanikarla-Marie, Michael Lam, David G Menter, Scott Kopetz
Platelets are cytoplasmic fragments generated by megakaryocytes in the bone marrow and do not possess a nucleus. They contribute to the "Circulome" consisting of all circulating cells, factors and macromolecules such as cfDNA. Their primary function is to recognize vascular lesions and initiate thrombus formation that ceases bleeding. This distinctive characteristic of platelets also contributes to cancer and its progression. The ability of platelets to recognize and interact with other cells and neighboring platelets enables them to interact with tumor cells in the circulation...
June 30, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28666287/the-impact-of-cfdna-screening-on-the-frequency-of-invasive-procedures-in-a-geographically-diverse-private-network
#18
Thomas J Garite, C Andrew Combs, Kimberly Maurel, Diana Abril, Anita Das
No abstract text is available yet for this article.
June 30, 2017: American Journal of Perinatology
https://www.readbyqxmd.com/read/28658993/influence-of-val16ala-sod2-polymorphism-on-sperm-quality-parameters
#19
Felipe Costa, Fernanda Barbisan, Charles Elias Assmann, Andressa Duarte Seehaber, Moisés Henrique Mastella Thiago Duarte, Marta Maria Medeiros Frescura Duarte, Ivana Beatrice Mânica da Cruz
The purpose of this study was to investigate the association between the Val16Ala superoxide dismutase manganese-dependent (SOD2) single nucleotide polymorphism (SNP) and sperm reproductive parameters in a sample of Brazilian men. A potential association between this polymorphism and some oxidative biochemical parameters as well as sperm plasma cell-free DNA (cfDNA) levels were also evaluated. The study was performed using semen samples obtained from male patients that had undergone semen analysis according to the 2010 World Health Organisation (WHO) recommendations and the Val16Ala-SOD2 SNP was genotyped by polymerase chain reaction (PCR)...
June 28, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28655575/cell-free-dna-in-a-three-dimensional-spheroid-cell-culture-model-a-preliminary-study
#20
Janine Aucamp, Carlemi Calitz, Abel J Bronkhorst, Krzysztof Wrzesinski, Sias Hamman, Chrisna Gouws, Piet J Pretorius
BACKGROUND: Investigating the biological functions of cell-free DNA (cfDNA) is limited by the interference of vast numbers of putative sources and causes of DNA release into circulation. Utilization of three-dimensional (3D) spheroid cell cultures, models with characteristics closer to the in vivo state, may be of significant benefit for cfDNA research. METHODS: CfDNA was isolated from the growth medium of C3A spheroid cultures in rotating bioreactors during both normal growth and treatment with acetaminophen...
June 24, 2017: International Journal of Biochemistry & Cell Biology
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